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#------------------------------------------------------------------------------
# File: MRC.pm
#
# Description: Read MRC (Medical Research Council) image files
#
# Revisions: 2021-04-21 - P. Harvey Created
#
# References: 1) https://www.ccpem.ac.uk/mrc_format/mrc2014.php
# 2) http://legacy.ccp4.ac.uk/html/library.html
# 3) https://github.com/ccpem/mrcfile/blob/master/mrcfile/dtypes.py
#
# Notes: The header is basically identical to the older CCP4 file format
#------------------------------------------------------------------------------
package Image::ExifTool::MRC;
use strict;
use vars qw($VERSION);
use Image::ExifTool qw(:DataAccess :Utils);
$VERSION = '1.00';
my %bool = (
Format => 'int8u',
PrintConv => { 0 => 'No', 1 => 'Yes' }
);
%Image::ExifTool::MRC::Main = (
PROCESS_PROC => \&Image::ExifTool::ProcessBinaryData,
GROUPS => { 0 => 'File', 1 => 'File', 2 => 'Image' },
VARS => { NO_LOOKUP => 1 }, # omit tags from lookup
FORMAT => 'int32u',
NOTES => q{
Tags extracted from Medical Research Council (MRC) format imaging files.
See L<https://www.ccpem.ac.uk/mrc_format/mrc2014.php> for the specification.
},
0 => 'ImageWidth',
1 => 'ImageHeight',
2 => {
Name => 'ImageDepth',
Notes => q{
number of sections. Use ExtractEmbedded option to extract metadata for all
sections
},
RawConv => '$$self{ImageDepth} = $val',
},
3 => {
Name => 'ImageMode',
PrintConv => {
0 => '8-bit signed integer',
1 => '16-bit signed integer',
2 => '32-bit signed real',
3 => 'complex 16-bit integer',
4 => 'complex 32-bit real',
6 => '16-bit unsigned integer',
},
},
4 => { Name => 'StartPoint', Format => 'int32u[3]' },
7 => { Name => 'GridSize', Format => 'int32u[3]' },
10 => { Name => 'CellWidth', Format => 'float', Notes => 'cell size in angstroms' },
11 => { Name => 'CellHeight',Format => 'float' },
12 => { Name => 'CellDepth', Format => 'float' },
13 => { Name => 'CellAlpha', Format => 'float' },
14 => { Name => 'CellBeta', Format => 'float' },
15 => { Name => 'CellGamma', Format => 'float' },
16 => { Name => 'ImageWidthAxis', PrintConv => { 1 => 'X', 2 => 'Y', 3 => 'Z' } },
17 => { Name => 'ImageHeightAxis', PrintConv => { 1 => 'X', 2 => 'Y', 3 => 'Z' } },
18 => { Name => 'ImageDepthAxis', PrintConv => { 1 => 'X', 2 => 'Y', 3 => 'Z' } },
19 => { Name => 'DensityMin', Format => 'float' },
20 => { Name => 'DensityMax', Format => 'float' },
21 => { Name => 'DensityMean',Format => 'float' },
22 => 'SpaceGroupNumber',
23 => { Name => 'ExtendedHeaderSize', RawConv => '$$self{ExtendedHeaderSize} = $val' },
26 => { Name => 'ExtendedHeaderType', Format => 'string[4]', RawConv => '$$self{ExtendedHeaderType} = $val' },
27 => 'MRCVersion',
49 => { Name => 'Origin', Format => 'float[3]' },
53 => { Name => 'MachineStamp', Format => 'int8u[4]', PrintConv => 'sprintf("0x%.2x 0x%.2x 0x%.2x 0x%.2x",split " ", $val)' },
54 => { Name => 'RMSDeviation', Format => 'float' },
55 => { Name => 'NumberOfLabels', RawConv => '$$self{NLab} = $val' },
56 => { Name => 'Label0', Format => 'string[80]', Condition => '$$self{NLab} > 0' },
76 => { Name => 'Label1', Format => 'string[80]', Condition => '$$self{NLab} > 1' },
96 => { Name => 'Label2', Format => 'string[80]', Condition => '$$self{NLab} > 2' },
116 => { Name => 'Label3', Format => 'string[80]', Condition => '$$self{NLab} > 3' },
136 => { Name => 'Label4', Format => 'string[80]', Condition => '$$self{NLab} > 4' },
156 => { Name => 'Label5', Format => 'string[80]', Condition => '$$self{NLab} > 5' },
176 => { Name => 'Label6', Format => 'string[80]', Condition => '$$self{NLab} > 6' },
196 => { Name => 'Label7', Format => 'string[80]', Condition => '$$self{NLab} > 7' },
216 => { Name => 'Label8', Format => 'string[80]', Condition => '$$self{NLab} > 8' },
236 => { Name => 'Label9', Format => 'string[80]', Condition => '$$self{NLab} > 9' },
);
%Image::ExifTool::MRC::FEI12 = (
PROCESS_PROC => \&Image::ExifTool::ProcessBinaryData,
GROUPS => { 0 => 'File', 1 => 'File', 2 => 'Image' },
VARS => { NO_LOOKUP => 1 }, # omit tags from lookup (way too many!)
NOTES => 'Tags extracted from FEI1 and FEI2 extended headers.',
0 => { Name => 'MetadataSize', Format => 'int32u', RawConv => '$$self{MetadataSize} = $val' },
4 => { Name => 'MetadataVersion', Format => 'int32u' },
8 => {
Name => 'Bitmask1',
Format => 'int32u',
RawConv => '$$self{BitM} = $val',
PrintConv => 'sprintf("0x%.8x", $val)',
},
12 => {
Name => 'TimeStamp',
Format => 'double',
Condition => '$$self{BitM} & 0x01',
Groups => { 2 => 'Time'},
# shift from days since Dec 30, 1899 to Unix epoch of Jan 1, 1970
# (my sample looks like local time, although it should be UTC)
ValueConv => 'ConvertUnixTime(($val-25569)*24*3600)',
PrintConv => '$self->ConvertDateTime($val)',
},
20 => { Name => 'MicroscopeType', Format => 'string[16]', Condition => '$$self{BitM} & 0x02' },
36 => { Name => 'MicroscopeID', Format => 'string[16]', Condition => '$$self{BitM} & 0x04' },
52 => { Name => 'Application', Format => 'string[16]', Condition => '$$self{BitM} & 0x08' },
68 => { Name => 'AppVersion', Format => 'string[16]', Condition => '$$self{BitM} & 0x10' },
84 => { Name => 'HighTension', Format => 'double', Condition => '$$self{BitM} & 0x20', Notes => 'volts' },
92 => { Name => 'Dose', Format => 'double', Condition => '$$self{BitM} & 0x40', Notes => 'electrons/m2' },
100 => { Name => 'AlphaTilt', Format => 'double', Condition => '$$self{BitM} & 0x80' },
108 => { Name => 'BetaTilt', Format => 'double', Condition => '$$self{BitM} & 0x100' },
116 => { Name => 'XStage', Format => 'double', Condition => '$$self{BitM} & 0x200' },
124 => { Name => 'YStage', Format => 'double', Condition => '$$self{BitM} & 0x400' },
132 => { Name => 'ZStage', Format => 'double', Condition => '$$self{BitM} & 0x800' },
140 => { Name => 'TiltAxisAngle', Format => 'double', Condition => '$$self{BitM} & 0x1000' },
148 => { Name => 'DualAxisRot', Format => 'double', Condition => '$$self{BitM} & 0x2000' },
156 => { Name => 'PixelSizeX', Format => 'double', Condition => '$$self{BitM} & 0x4000' },
164 => { Name => 'PixelSizeY', Format => 'double', Condition => '$$self{BitM} & 0x8000' },
220 => { Name => 'Defocus', Format => 'double', Condition => '$$self{BitM} & 0x400000' },
228 => { Name => 'STEMDefocus', Format => 'double', Condition => '$$self{BitM} & 0x800000' },
236 => { Name => 'AppliedDefocus', Format => 'double', Condition => '$$self{BitM} & 0x1000000' },
244 => { Name => 'InstrumentMode', Format => 'int32u', Condition => '$$self{BitM} & 0x2000000', PrintConv => { 1 => 'TEM', 2 => 'STEM' } },
248 => { Name => 'ProjectionMode', Format => 'int32u', Condition => '$$self{BitM} & 0x4000000', PrintConv => { 1 => 'Diffraction', 2 => 'Imaging' } },
252 => { Name => 'ObjectiveLens', Format => 'string[16]', Condition => '$$self{BitM} & 0x8000000' },
268 => { Name => 'HighMagnificationMode', Format => 'string[16]', Condition => '$$self{BitM} & 0x10000000' },
284 => { Name => 'ProbeMode', Format => 'int32u', Condition => '$$self{BitM} & 0x20000000', PrintConv => { 1 => 'Nano', 2 => 'Micro' } },
288 => { Name => 'EFTEMOn', %bool, Condition => '$$self{BitM} & 0x40000000' },
289 => { Name => 'Magnification', Format => 'double', Condition => '$$self{BitM} & 0x80000000' },
297 => {
Name => 'Bitmask2',
Format => 'int32u',
RawConv => '$$self{BitM} = $val',
PrintConv => 'sprintf("0x%.8x", $val)',
},
301 => { Name => 'CameraLength', Format => 'double', Condition => '$$self{BitM} & 0x01' },
309 => { Name => 'SpotIndex', Format => 'int32u', Condition => '$$self{BitM} & 0x02' },
313 => { Name => 'IlluminationArea',Format => 'double', Condition => '$$self{BitM} & 0x04' },
321 => { Name => 'Intensity', Format => 'double', Condition => '$$self{BitM} & 0x08' },
329 => { Name => 'ConvergenceAngle',Format => 'double', Condition => '$$self{BitM} & 0x10' },
337 => { Name => 'IlluminationMode',Format => 'string[16]', Condition => '$$self{BitM} & 0x20' },
353 => { Name => 'WideConvergenceAngleRange', %bool, Condition => '$$self{BitM} & 0x40' },
354 => { Name => 'SlitInserted', %bool, Condition => '$$self{BitM} & 0x80' },
355 => { Name => 'SlitWidth', Format => 'double', Condition => '$$self{BitM} & 0x100' },
363 => { Name => 'AccelVoltOffset', Format => 'double', Condition => '$$self{BitM} & 0x200' },
371 => { Name => 'DriftTubeVolt', Format => 'double', Condition => '$$self{BitM} & 0x400' },
379 => { Name => 'EnergyShift', Format => 'double', Condition => '$$self{BitM} & 0x800' },
387 => { Name => 'ShiftOffsetX', Format => 'double', Condition => '$$self{BitM} & 0x1000' },
395 => { Name => 'ShiftOffsetY', Format => 'double', Condition => '$$self{BitM} & 0x2000' },
403 => { Name => 'ShiftX', Format => 'double', Condition => '$$self{BitM} & 0x4000' },
411 => { Name => 'ShiftY', Format => 'double', Condition => '$$self{BitM} & 0x8000' },
419 => { Name => 'IntegrationTime', Format => 'double', Condition => '$$self{BitM} & 0x10000' },
427 => { Name => 'BinningWidth', Format => 'int32u', Condition => '$$self{BitM} & 0x20000' },
431 => { Name => 'BinningHeight', Format => 'int32u', Condition => '$$self{BitM} & 0x40000' },
435 => { Name => 'CameraName', Format => 'string[16]', Condition => '$$self{BitM} & 0x80000' },
451 => { Name => 'ReadoutAreaLeft', Format => 'int32u', Condition => '$$self{BitM} & 0x100000' },
455 => { Name => 'ReadoutAreaTop', Format => 'int32u', Condition => '$$self{BitM} & 0x200000' },
459 => { Name => 'ReadoutAreaRight',Format => 'int32u', Condition => '$$self{BitM} & 0x400000' },
463 => { Name => 'ReadoutAreaBottom',Format=> 'int32u', Condition => '$$self{BitM} & 0x800000' },
467 => { Name => 'CetaNoiseReduct', %bool, Condition => '$$self{BitM} & 0x1000000' },
468 => { Name => 'CetaFramesSummed',Format => 'int32u', Condition => '$$self{BitM} & 0x2000000' },
472 => { Name => 'DirectDetElectronCounting', %bool, Condition => '$$self{BitM} & 0x4000000' },
473 => { Name => 'DirectDetAlignFrames', %bool, Condition => '$$self{BitM} & 0x8000000' },
490 => {
Name => 'Bitmask3',
Format => 'int32u',
RawConv => '$$self{BitM} = $val',
PrintConv => 'sprintf("0x%.8x", $val)',
},
518 => { Name => 'PhasePlate', %bool, Condition => '$$self{BitM} & 0x40' },
519 => { Name => 'STEMDetectorName',Format => 'string[16]', Condition => '$$self{BitM} & 0x80' },
535 => { Name => 'Gain', Format => 'double', Condition => '$$self{BitM} & 0x100' },
543 => { Name => 'Offset', Format => 'double', Condition => '$$self{BitM} & 0x200' },
571 => { Name => 'DwellTime', Format => 'double', Condition => '$$self{BitM} & 0x8000' },
579 => { Name => 'FrameTime', Format => 'double', Condition => '$$self{BitM} & 0x10000' },
587 => { Name => 'ScanSizeLeft', Format => 'int32u', Condition => '$$self{BitM} & 0x20000' },
591 => { Name => 'ScanSizeTop', Format => 'int32u', Condition => '$$self{BitM} & 0x40000' },
595 => { Name => 'ScanSizeRight', Format => 'int32u', Condition => '$$self{BitM} & 0x80000' },
599 => { Name => 'ScanSizeBottom', Format => 'int32u', Condition => '$$self{BitM} & 0x100000' },
603 => { Name => 'FullScanFOV_X', Format => 'double', Condition => '$$self{BitM} & 0x200000' },
611 => { Name => 'FullScanFOV_Y', Format => 'double', Condition => '$$self{BitM} & 0x400000' },
619 => { Name => 'Element', Format => 'string[16]', Condition => '$$self{BitM} & 0x800000' },
635 => { Name => 'EnergyIntervalLower', Format => 'double', Condition => '$$self{BitM} & 0x1000000' },
643 => { Name => 'EnergyIntervalHigher',Format => 'double', Condition => '$$self{BitM} & 0x2000000' },
651 => { Name => 'Method', Format=> 'int32u', Condition => '$$self{BitM} & 0x4000000' },
655 => { Name => 'IsDoseFraction', %bool, Condition => '$$self{BitM} & 0x8000000' },
656 => { Name => 'FractionNumber', Format => 'int32u', Condition => '$$self{BitM} & 0x10000000' },
660 => { Name => 'StartFrame', Format => 'int32u', Condition => '$$self{BitM} & 0x20000000' },
664 => { Name => 'EndFrame', Format => 'int32u', Condition => '$$self{BitM} & 0x40000000' },
668 => { Name =>'InputStackFilename',Format=> 'string[80]', Condition => '$$self{BitM} & 0x80000000' },
748 => {
Name => 'Bitmask4',
Format => 'int32u',
RawConv => '$$self{BitM} = $val',
PrintConv => 'sprintf("0x%.8x", $val)',
},
752 => { Name => 'AlphaTiltMin', Format => 'double', Condition => '$$self{BitM} & 0x01' },
760 => { Name => 'AlphaTiltMax', Format => 'double', Condition => '$$self{BitM} & 0x02' },
#
# FEI2 header starts here
#
768 => { Name => 'ScanRotation', Format => 'double', Condition => '$$self{BitM} & 0x04' },
776 => { Name => 'DiffractionPatternRotation',Format=>'double', Condition => '$$self{BitM} & 0x08' },
784 => { Name => 'ImageRotation', Format => 'double', Condition => '$$self{BitM} & 0x10' },
792 => { Name => 'ScanModeEnumeration',Format => 'int32u', Condition => '$$self{BitM} & 0x20', PrintConv => { 0 => 'Other', 1 => 'Raster', 2 => 'Serpentine' } },
796 => {
Name => 'AcquisitionTimeStamp',
Format => 'int64u',
Condition => '$$self{BitM} & 0x40',
Groups => { 2 => 'Time' },
# microseconds since 1970 UTC
ValueConv => 'ConvertUnixTime($val / 1e6, 1, 6)',
PrintConv => '$self->ConvertDateTime($val)',
},
804 => { Name => 'DetectorCommercialName', Format => 'string[16]', Condition => '$$self{BitM} & 0x80' },
820 => { Name => 'StartTiltAngle', Format => 'double', Condition => '$$self{BitM} & 0x100' },
828 => { Name => 'EndTiltAngle', Format => 'double', Condition => '$$self{BitM} & 0x200' },
836 => { Name => 'TiltPerImage', Format => 'double', Condition => '$$self{BitM} & 0x400' },
844 => { Name => 'TitlSpeed', Format => 'double', Condition => '$$self{BitM} & 0x800' },
852 => { Name => 'BeamCenterX', Format => 'int32u', Condition => '$$self{BitM} & 0x1000' },
856 => { Name => 'BeamCenterY', Format => 'int32u', Condition => '$$self{BitM} & 0x2000' },
860 => {
Name => 'CFEGFlashTimeStamp',
Format => 'int64u',
Condition => '$$self{BitM} & 0x4000',
Groups => { 2 => 'Time' },
ValueConv => 'ConvertUnixTime($val / 1e6, 1, 6)',
PrintConv => '$self->ConvertDateTime($val)',
},
868 => { Name => 'PhasePlatePosition',Format => 'int32u', Condition => '$$self{BitM} & 0x8000' },
872 => { Name => 'ObjectiveAperture', Format=>'string[16]',Condition => '$$self{BitM} & 0x10000' },
);
#------------------------------------------------------------------------------
# Extract metadata from a MRC image
# Inputs: 0) ExifTool object reference, 1) dirInfo reference
# Returns: 1 on success, 0 if this wasn't a valid MRC file
sub ProcessMRC($$)
{
my ($et, $dirInfo) = @_;
my $raf = $$dirInfo{RAF};
my ($buff, $tagTablePtr, $i);
# verify this is a valid MRC file
return 0 unless $raf->Read($buff, 1024) == 1024;
# validate axes, "MAP" file type and machine stamp
return 0 unless $buff =~ /^.{64}[\x01\x02\x03]\0\0\0[\x01\x02\x03]\0\0\0[\x01\x02\x03]\0\0\0.{132}MAP[\0 ](\x44\x44|\x44\x41|\x11\x11)\0\0/s;
$et->SetFileType();
SetByteOrder('II');
my %dirInfo = (
DataPt => \$buff,
DirStart => 0,
DirLen => length($buff),
);
$tagTablePtr = GetTagTable('Image::ExifTool::MRC::Main');
$et->ProcessDirectory(\%dirInfo, $tagTablePtr);
# (I don't have any samples with extended headers for testing, so these are not yet decoded)
if ($$et{ExtendedHeaderSize} and $$et{ExtendedHeaderType} =~ /^FEI[12]/) {
unless ($raf->Read($buff,4)==4 and $raf->Seek(-4,1)) { # read metadata size
$et->Warn('Error reading extended header');
return 1;
}
my $size = Get32u(\$buff, 0);
if ($size * $$et{ImageDepth} > $$et{ExtendedHeaderSize}) {
$et->Warn('Corrupted extended header');
return 1;
}
$dirInfo{DirLen} = $size;
$tagTablePtr = GetTagTable('Image::ExifTool::MRC::FEI12');
for ($i=0; ;) {
$dirInfo{DataPos} = $raf->Tell();
$raf->Read($buff, $size) == $size or $et->Warn("Error reading extended header $i"), last;
$et->ProcessDirectory(\%dirInfo, $tagTablePtr);
last if ++$i >= $$et{ImageDepth};
unless ($$et{OPTIONS}{ExtractEmbedded}) {
$et->Warn('Use the ExtractEmbedded option to read metadata for all frames',3);
last;
}
$$et{DOC_NUM} = ++$$et{DOC_COUNT};
}
delete $$et{DOC_NUM};
}
return 1;
}
1; # end
__END__
=head1 NAME
Image::ExifTool::MRC - Read MRC meta information
=head1 SYNOPSIS
This module is used by Image::ExifTool
=head1 DESCRIPTION
This module contains definitions required by Image::ExifTool to read
metadata from Medical Research Council (MRC) images.
=head1 AUTHOR
Copyright 2003-2023, Phil Harvey (philharvey66 at gmail.com)
This library is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
=head1 REFERENCES
=over 4
=item L<https://www.ccpem.ac.uk/mrc_format/mrc2014.php>
=item L<http://legacy.ccp4.ac.uk/html/library.html>
=item L<https://github.com/ccpem/mrcfile/blob/master/mrcfile/dtypes.py>
=back
=head1 SEE ALSO
L<Image::ExifTool::TagNames/MRC Tags>,
L<Image::ExifTool(3pm)|Image::ExifTool>
=cut
|
